Cisco WLAN controller with AP’s at remote sites.

I have setup WLAN controllers before on local sites no problem before but I have a new job coming up where I need to install a WLAN controller at a datacentre and then all the lightweight AP’s will be at remote sites connected via an MPLS WAN (full any to any routing)
All the traffic is datacentre bound (all apps etc are hosted there) so there is no back and forth for local traffic.
The question I have is how to you ‘discover’ the access points on layer 3, I’ve done this before on local networks and the controller just picks up the AP’s on layer 2 fine but with this new scenario I dont fully understand how you get the controller to ‘see’ the access points?